[gnuastro-commits] master 0b10ab7: Book: Corrections and edits to the Sufi tutorial

[Mohammad Akhlaghi]

branch: master
commit 0b10ab7b0d28f92bb427b3eecfb1d527d9cbbe6f
Author: Mohammad Akhlaghi <address@hidden>
Commit: Mohammad Akhlaghi <address@hidden>

    Book: Corrections and edits to the Sufi tutorial
    
    Hamed Altafi pointed out a few typos in this tutorial (mainly things we
    forgot to update after the program's new features), and had some advice
    (e.g., not introducing Sufi at the start of the tutorial, and advising
    caution when copying the catalog from the PDF book).
    
    With this commit, all the raised points have been implemented.
---
 THANKS                       |  1 +
 doc/announce-acknowledge.txt |  1 +
 doc/gnuastro.texi            | 66 ++++++++++++++++++++++----------------------
 3 files changed, 35 insertions(+), 33 deletions(-)

diff --git a/THANKS b/THANKS
index 069d240..90a71a5 100644
--- a/THANKS
+++ b/THANKS
@@ -20,6 +20,7 @@ support in Gnuastro. The list is ordered alphabetically (by 
family name).
 
     Valentina Abril-melgarejo            address@hidden
     Marjan Akbari                        address@hidden
+    Hamed Altafi                         address@hidden
     Roland Bacon                         address@hidden
     Roberto Baena Gallé                  address@hidden
     Karl Berry                           address@hidden
diff --git a/doc/announce-acknowledge.txt b/doc/announce-acknowledge.txt
index 7e123c6..9479f9b 100644
--- a/doc/announce-acknowledge.txt
+++ b/doc/announce-acknowledge.txt
@@ -1,5 +1,6 @@
 Alphabetically ordered list to acknowledge in the next release.
 
+Hamed Altafi
 Leindert Boogaard
 Raul Infante-Sainz
 Lee Kelvin
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index cf7d3f3..1f1ba32 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -1889,23 +1889,22 @@ use in the example codes through the book, please see 
@ref{Conventions}.
 @cindex Azophi
 @cindex Abd al-rahman Sufi
 @cindex Sufi, Abd al-rahman
-It is the year 953 A.D.  and address@hidden al-rahman Sufi (903 --
-986 A.D.), also known in Latin as Azophi was an Iranian
+It is the year 953 A.D. and Abd al-rahman Sufi (903 -- 986
+A.D.)@footnote{In Latin Sufi is known as Azophi. He was an Iranian
 astronomer. His manuscript ``Book of fixed stars'' contains the first
-recorded observations of the Andromeda galaxy, the Large Magellanic
-Cloud and seven other non-stellar or `nebulous' objects.}  is in
-Shiraz as a guest astronomer. He had come there to use the advanced
-123 centimeter astrolabe for his studies on the Ecliptic. However,
-something was bothering him for a long time. While mapping the
-constellations, there were several non-stellar objects that he had
-detected in the sky, one of them was in the Andromeda
-constellation. During a trip he had to Yemen, Sufi had seen another
-such object in the southern skies looking over the Indian ocean. He
-wasn't sure if such cloud-like non-stellar objects (which he was the
-first to call address@hidden' in Arabic or `nebulous') were real
-astronomical objects or if they were only the result of some bias in
-his observations. Could such diffuse objects actually be detected at
-all with his detection technique?
+recorded observations of the Andromeda galaxy, the Large Magellanic Cloud
+and seven other non-stellar or `nebulous' objects.}  is in Shiraz as a
+guest astronomer. He had come there to use the advanced 123 centimeter
+astrolabe for his studies on the Ecliptic. However, something was bothering
+him for a long time. While mapping the constellations, there were several
+non-stellar objects that he had detected in the sky, one of them was in the
+Andromeda constellation. During a trip he had to Yemen, Sufi had seen
+another such object in the southern skies looking over the Indian ocean. He
+wasn't sure if such cloud-like non-stellar objects (which he was the first
+to call address@hidden' in Arabic or `nebulous') were real astronomical
+objects or if they were only the result of some bias in his
+observations. Could such diffuse objects actually be detected at all with
+his detection technique?
 
 @cindex Almagest
 @cindex Claudius Ptolemy
@@ -2028,10 +2027,11 @@ Using all the information above, he creates the catalog 
of mock profiles he
 wants in a file named @file{cat.txt} (short for catalog) using his favorite
 text editor and stores it in a directory named @file{simulationtest} in his
 home directory. [The @command{cat} command prints the contents of a file,
-short for concatenation. So please copy-paste the lines after
+short for ``concatenation''. So please copy-paste the lines after
 address@hidden cat.txt}'' into @file{cat.txt} when the editor opens in the
 steps above it, note that there are 7 lines, first one starting with
address@hidden:
address@hidden Also be careful when copying from the PDF format, the Info, web,
+or text formats shouldn't have any problem]:
 
 @example
 $ mkdir ~/simulationtest
@@ -2105,6 +2105,7 @@ Convolve started on Mon Apr  6 16:35:32 953
   - Multiplied in the frequency domain.                0.040659 seconds
   - Converted back to the spatial domain.              3.465344 seconds
   - Padded parts removed.                              0.016767 seconds
+  - Output: cat_convolved.fits
 Convolve finished in:  10.422161 seconds
 
 $ls
@@ -2117,9 +2118,9 @@ and showed the effect of convolution to his student and 
explained to him
 how a PSF with a larger FWHM would make the points even wider. With the
 convolved image ready, they were prepared to re-sample it to the original
 pixel scale Sufi had planned [from the @command{$ astmkprof -P} command
-above, recall that MakeProfiles had over-sampled the image by 5 times]. Sufi
-explained the basic concepts of warping the image to his student and ran
-Warp with the following command:
+above, recall that MakeProfiles had over-sampled the image by 5
+times]. Sufi explained the basic concepts of warping the image to his
+student and ran Warp with the following command:
 
 @example
 $ astwarp --scale=1/5 --centeroncorner cat_convolved.fits
@@ -2142,12 +2143,12 @@ NAXIS2  =                  526 / length of data axis 2
 @end example
 
 @noindent
address@hidden now has the correct pixel scale. However,
address@hidden now has the correct pixel scale. However,
 the image is still larger than what we had wanted, it is 526
 (@mymath{500+13+13}) by 526 pixels. The student is slightly confused, so
-Sufi also re-samples the PSF with the same scale and shows him that it is 27
-(@mymath{2\times13+1}) by 27 pixels. Sufi goes on to explain how frequency
-space convolution will dim the edges and that is why he added the
+Sufi also re-samples the PSF with the same scale and shows him that it is
+27 (@mymath{2\times13+1}) by 27 pixels. Sufi goes on to explain how
+frequency space convolution will dim the edges and that is why he added the
 @option{--prepforconv} option to MakeProfiles, see @ref{If convolving
 afterwards}. Now that convolution is done, Sufi can remove those extra
 pixels using Crop with the command below. Crop's @option{--section} option
@@ -2156,7 +2157,7 @@ standard), so the crop's first pixel has to be 14, not 13.
 
 @example
 $ astcrop cat_convolved_scaled.fits --section=14:*-13,14:*-13    \
-          --zeroisnotblank
+          --mode=img --zeroisnotblank
 Crop started on Sat Oct  6 17:03:24 953
   - Read metadata of 1 image.                          0.001304 seconds
   ---- ...nvolved_scaled_cropped.fits created: 1 input.
@@ -2180,7 +2181,7 @@ ran MakeNoise:
 
 @example
 $ astmknoise --zeropoint=18 --background=7 --output=out.fits    \
-             cat_convolved_warped_crop.fits
+             cat_convolved_scaled_crop.fits
 MakeNoise started on Mon Apr  6 17:05:06 953
   - Generator type: mt19937
   - Generator seed: 1428318100
@@ -2251,12 +2252,11 @@ He used this chance to remind the student of the 
importance of comments in
 code or shell scripts: when writing the code, you have a good mental
 picture of what you are doing, so writing comments might seem superfluous
 and excessive. However, in one month when you want to re-use the script,
-you have lost that mental picture and rebuilding it is can be
-time-consuming and frustrating. The importance of comments is further
-amplified when you want to share the script with a friend/colleague. So it
-is good to accompany any script/code with useful comments while you are
-writing it (have a good mental picture of what/why you are doing
-something).
+you have lost that mental picture and remembering it can be time-consuming
+and frustrating. The importance of comments is further amplified when you
+want to share the script with a friend/colleague. So it is good to
+accompany any script/code with useful comments while you are writing it
+(create a good mental picture of what/why you are doing something).
 
 @cindex Gedit
 @cindex GNU Emacs